Browse
Submit Data
Databases
API
Help

Dataset Information

317 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RBDmap - The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

ABSTRACT: RBDmap protein regions contacting RNA were crosslinked with UV and captured with oligodT beads

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture, Cardiac Muscle Cell

SUBMITTER: Sophia Foehr

LAB HEAD: Jeroen Krijgsveld

PROVIDER: PXD002543 | Pride | 2016-08-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	140124_CF_YL_RBDmap_rep1_f1_40p.raw	Raw
	140124_CF_YL_RBDmap_rep1_f2_40p.raw	Raw
	140124_CF_YL_RBDmap_rep1_f3_40p.raw	Raw
	140124_CF_YL_RBDmap_rep1_f4_40p.raw	Raw
	140124_CF_YL_RBDmap_rep1_f5_40p.raw	Raw

Items per page:

1 - 5 of 25

Publications

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease.

Liao Yalin Y Castello Alfredo A Fischer Bernd B Leicht Stefan S Föehr Sophia S Frese Christian K CK Ragan Chikako C Kurscheid Sebastian S Pagler Eloisa E Yang Hao H Krijgsveld Jeroen J Hentze Matthias W MW Preiss Thomas T

Cell reports 20160721 5

RNA functions through the dynamic formation of complexes with RNA-binding proteins (RBPs) in all clades of life. We determined the RBP repertoire of beating cardiomyocytic HL-1 cells by jointly employing two in vivo proteomic methods, mRNA interactome capture and RBDmap. Together, these yielded 1,148 RBPs, 391 of which are shared with all other available mammalian RBP repertoires, while 393 are thus far unique to cardiomyocytes. RBDmap further identified 568 regions of RNA contact within 368 RBP ...[more]

PMID: 27452465

Similar Datasets

Genome-wide identification of protein binding sites on RNAs in mammalian cells [PBS-R]

Project description:We develop a novel method, called protein binding sites on RNA (PBS-R) to identify genome-wide protein binding sites on RNAs without using antibodies. Double click strategy is used for the PBS-R assay. Proteins and RNAs are UV-crosslinked in vivo first, then the proteins are crosslinked to the magnetic beads. The protein binding RNA elements are captured, reverse transcribed and sequenced.

2018-11-10 | GSE121919 | GEO

RNA-seq of miR-CLIP double purified, miR-124/miR-132 miR-CLIP probe treated HEK293T cells and corresponding mock treated and intermediate samples

Project description:Targetome of miR-124/miR-132 was enriched in HEK293T cells, a cell line which lacks the expression of these miRNA. The targetome was captured using miR-CLIP, a transfection-based double-purification crosslinking and immunoprecipitation (CLIP) method. Therefore HEK293T cells were transfected with miR-124/miR-132 miR-CLIP probes, which are trioxsalen, biotin bis-modified pre-miRNAs. Unspecific RNA-protein and trioxsalen mediated RNA-RNA crosslinking were induced by UV-irradiation before cell lysis. Total RNA (input samples) was enriched for AGO2-bound RNA using AGO2 immunoprecipitation, by depleting non-RISC associated RNAs. A second enrichment for specific targets of the transfected miRNA is performed using magnetic streptavidin-beads. This step relies on the interaction of the biotinylated probe, on which the RNA target is crosslinked, with the beads. The method was shown to deliver high-quality miRNA targetomes of both 5p and 3p miRNAs.

2020-11-23 | E-MTAB-8517 | biostudies-arrayexpress

HL-1 mRNA interactome - The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

Project description:RNAsfunction as compositionally diverse ribonucleoprotein (RNP) comlplexes, formed through interactions with RNA-binding proteins (RBPs). We explored the murine cardiomyocyte RBP repertoire.

2016-08-17 | PXD002541 | Pride

Differential Protein Occupancy Profiling of the mRNA Transcriptome

Project description:Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We have developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing (Baltz and Munschauer et al. 2012). Our current work focuses on streamlining and extending protein occupancy profiling on poly(A)-RNA. Our objectives are to identify previously unknown protein-bound transcripts and, more importantly, to assess global and local differences in protein occupancy across different biological conditions. To this end, we have implemented poppi, the first pipeline for differential analysis of protein occupancy profiles. We have applied our analysis pipeline to pinpoint changes in occupancy profiles of MCF7 cells against already published HEK293 cells. We generated protein occupancy cDNA libraries for two biological replicates. Briefly, we crosslinked 4SU-labeled MCF7 cells and purified protein-mRNA complexes using oligo(dT)-beads. The precipitate was treated with RNAse I to reduce the protein-crosslinked RNA fragments to a length of about 30-60 nt. To remove non-crosslinked RNA, protein-RNA complexes were precipitated with ammonium sulfate and blotted onto nitrocellulose. The RNA was recovered by Proteinase K treatment, ligated to cloning adapters, and reverse transcribed. The resulting cDNA libraries were PCR-amplified and next-generation sequenced.

2013-12-05 | E-GEOD-49831 | biostudies-arrayexpress

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease.

Project description:RNA functions through the dynamic formation of complexes with RNA-binding proteins (RBPs) in all clades of life. We determined the RBP repertoire of beating cardiomyocytic HL-1 cells by jointly employing two in vivo proteomic methods, mRNA interactome capture and RBDmap. Together, these yielded 1,148 RBPs, 391 of which are shared with all other available mammalian RBP repertoires, while 393 are thus far unique to cardiomyocytes. RBDmap further identified 568 regions of RNA contact within 368 RBPs. The cardiomyocyte mRNA interactome composition reflects their unique biology. Proteins with roles in cardiovascular physiology or disease, mitochondrial function, and intermediary metabolism are all highly represented. Notably, we identified 73 metabolic enzymes as RBPs. RNA-enzyme contacts frequently involve Rossmann fold domains with examples in evidence of both, mutual exclusivity of, or compatibility between RNA binding and enzymatic function. Our findings raise the prospect of previously hidden RNA-mediated regulatory interactions among cardiomyocyte gene expression, physiology, and metabolism.

| S-EPMC4977271 | biostudies-literature

CAPRI RNA binding proteins and domains in Drosophila and Humans

Project description:In the current work, we present a comprehensive coverage of the RNA-binding protein (RBP) interactome of Drosophila at four levels of resolution. The highest level tackled in our study represents the RNA-protein complexes, which we address by combining formaldehyde crosslinking of Drosophila S2 cells followed by polyA+ pulldown using oligo-dT beads. On the second level of resolution we identified direct RBPs in the cell using UV crosslinking. Given the paucity of information available on the RNA-binding regions in the Drosophila RBPs that we uncovered, we developed the CAPRI methodology to dissect RNA binding domains (RBDs) on a systematic level. The CAPRI technique provided the final two levels of resolution of our study. The protocol utilised FASP to enable isolation of peptides crosslinked to RNA and peptides adjacent to these crosslinked sites. The CAPRI pipeline mapped both the peptides in proximity to RNA and the precise amino acids contacting RNA. The RNA crosslinked peptide analysis was made by de novo peptide analysis software, PEAKS (Bioinformatics Solutions Inc). In a separate analysis, we also applied FA crosslinking to RBD capture and showed it to be a viable complementary method to the CAPRI workflow. We next applied CAPRI interactome capture to human cells in order to analyse the evolutionary conservation of newly identified RNA binding domains between the two species. These interactome capture techniques and the datasets acquired using them are discussed in detail in the following sections. In summary, we present a comprehensive resource for the study of RNA-protein interactions at a high throughput scale.

2019-07-02 | PXD013338 | Pride

LRRC10 regulates mammalian cardiomyocyte cell cycle exit and heart regeneration

Project description:Bulk RNA expression profiles were captured from hearts of Leucine-rich repeat containing protein 10 (Lrrc10) knockout (KO) and wild type (WT) mice that underwent myocardial infarction (MI) or sham (SH) surgery at postnatal day 1 and full ventricle collection at 7 days post-surgery

2023-07-10 | GSE221539 | GEO

An Immunological Synapse Formation Between T Regulatory Cells and Cancer-Associated Fibroblasts Promotes Tumour Development

Project description:The cells were lysed in a buffer consisting of 4% SDS, 0.1 M DTT, 100 mM Tris/HCl; pH 7.6 and heated for 5 minutes at 99℃. The protein extracts were processed according to theSp3 protocol. The reduced cysteine residues were alkylated in 200 mM iodoacetamide (Acros Organics). 20 μg of beads (1:1 mixture of hydrophilic and hydrophobic SeraMag carboxylate-modified beads; GE Life Sciences) were added to each sample in 50% ethanol. Protein clean-up was performed on a magnetic rack. The beads were washed twice with 80% ethanol followed by one wash with 100% acetonitrile (Fisher Chemical). The beads-captured proteins were digested overnight at 37 ℃ with 0.5 μg trypsin/LysC mix in 25 mM ammonium bicarbonate under vigorous shaking (1200 rpm, Eppendorf Thermomixer). The supernatants were collected and the peptides were purified by a modified Sp3 clean-up protocol and finally solubilized in the mobile phase A (0.1% formic acid in water), and sonicated. Peptide concentration was determined through absorbance measurement at 280 nm using a nanodrop instrument.

2024-05-08 | PXD047024 | Pride

PDAP1 RIP in UV-crosslinked human T cells

Project description:PDAP1 RIP in UV-crosslinked human T cells

| PRJNA761680 | ENA

UPA-Seq: Prediction of functional lncRNAs using the sensitivities to UV-crosslinking

Project description:Assuming that functional lncRNAs form larger ribonucleoprotein complex and thus are easily crosslinked to proteins upon UV-irradiation, we performed RNA-Seq analyses of RNAs recovered from the aqueous phase after the UV-irradiation and phenol chloroform extraction (UPA-Seq)

2018-09-21 | GSE114789 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data